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Hi,
I am trying to repeat this tutorial: https://github.com/MobleyLab/drug-computing/blob/f38a4148e9e70238c88fc8110d95b34688f02838/uci-pharmsci/lectures/SMIRNOFF_simulations/mixture_simulations.ipynb…
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### Bug summary
When running for other complex its working for few system not working giving following error.
I run some MD simulation with Gromacs 2023 for them its working. The md simulation exe…
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### My Question is...
I am currently facing an issue while attempting to run protein-ligand binding free energy calculations embedded in a membrane using CHARMM force field files via the gmx_MMPBSA t…
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Hello,
I'm using qubekit to do some testing work. The program stopped at the "torsion_optimisation" stage.
The input molecule is a glycine.
, partial charge methods fail. This is either from `antechamber` or possibly `sqm` and probably related to issues that…
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### Bug summary
When I execute the an mmgbsa run, the run proceeds through calculating the complex, receptor and ligand contributions, but then fails at "Parsing results to output files..." saying th…
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**Describe the bug**
`Molecule.enumerate_stereoisomers()` fails on some molecules with the OpenEye toolkit backend.
**To Reproduce**
Here is an example:
```python
>>> from openff.toolkit.topolo…